bio-ucsc-api 0.3.1 → 0.4.0

data/lib/bio-ucsc/tetnig2/db_connection.rb

@@ -1,57 +0,0 @@
-#
-# = db_connection.rb - UCSC DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# Copyright::   Copyright (C) 2010
-#               Jan Aerts <jan.aerts@gmail.com>
-# License::     Ruby licence (Ryby's / GPLv2 dual)
-
-require 'rubygems'
-require 'active_record'
-
-module Bio
-  module Ucsc
-
-    module TetNig2
-      DATABASE_NAME = "tetNig2"
-
-      # = DESCRIPTION
-      # Actual connection established to the UCSC mysql server.
-      class DBConnection < ActiveRecord::Base
-        # = DESCRIPTION
-        # The #connect method make the connection
-        #
-        # = USAGE
-        # Bin::Ucsc::DB_NAME::DBConnection.connect
-        #
-        # ---
-        # *Arguments*: none
-        @@db_adapter  ||= 'mysql'
-        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
-        @@db_username ||= 'genome'
-        @@db_password ||= ''
-
-        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
-
-        self.abstract_class = true
-
-        def self.default
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => DATABASE_NAME,
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/uniprot/db_connection.rb

@@ -1,59 +0,0 @@
-#
-# = lib/ucsc/uniprot/db_connection.rb - UCSC UniProt DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# Copyright::   Copyright (C) 2010
-#               Jan Aerts <jan.aerts@gmail.com>
-# License::     Ruby licence (Ryby's / GPLv2 dual)
-
-require 'rubygems'
-require 'active_record'
-
-module Bio
-  module Ucsc
-
-    module UniProt
-      # = DESCRIPTION
-      # The Ucsc::Uniplot::DBConnection is the actual connection established
-      # with the UCSC mysql server.
-
-      class DBConnection < ActiveRecord::Base
-        # = DESCRIPTION
-        # The Bin::Ucsc::Uniplot::DBConnection#connect method makes the connection
-        # to the UCSC uniprot database.
-        #
-        # = USAGE
-        #  # Connect to the uniplot
-        #  Bin::Ucsc::Uniprot::DBConnection.connect
-        #
-        # ---
-        # *Arguments*: none
-        @@db_adapter  ||= 'mysql'
-        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
-        @@db_username ||= 'genome'
-        @@db_password ||= ''
-
-        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
-
-        self.abstract_class = true
-
-        def self.default
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => 'uniProt',
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module Uniprot
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/visigene/db_connection.rb

@@ -1,55 +0,0 @@
-#
-# = db_connection.rb - UCSC DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# Copyright::   Copyright (C) 2010
-#               Jan Aerts <jan.aerts@gmail.com>
-# License::     Ruby licence (Ryby's / GPLv2 dual)
-
-require 'rubygems'
-require 'active_record'
-
-module Bio
-  module Ucsc
-
-    module VisiGene
-      # = DESCRIPTION
-      # Actual connection established to the UCSC mysql server.
-      class DBConnection < ActiveRecord::Base
-        # = DESCRIPTION
-        # The #connect method make the connection
-        #
-        # = USAGE
-        #  Bin::Ucsc::DB_NAME::DBConnection.connect
-        #
-        # ---
-        # *Arguments*: none
-        @@db_adapter  ||= 'mysql'
-        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
-        @@db_username ||= 'genome'
-        @@db_password ||= ''
-
-        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
-
-        self.abstract_class = true
-
-        def self.default
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => 'visiGene',
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/xentro2/chaingalgal3.rb

@@ -1,81 +0,0 @@
-# Copyright::
-#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
-#
-# In the hg18 database, this table is actually separated
-# into "chr1_*", "chr2_*", etc. This class dynamically
-# define *::Chr1_*, *::Chr2_*, etc. The
-# Rmsk.find_by_interval calls an appropreate class automatically.
-
-module Bio
-  module Ucsc
-    module TaeGut1
-
-      class ChainGalGal3
-        KLASS = "ChainGalGal3"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
-          class_eval %!
-            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
-
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-        
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
-
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
-                zstart = interval.zero_start
-                zend   = interval.zero_end
-                if opt[:partial] == true
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
- OR  (tEnd BETWEEN :zstart AND :zend)
- OR  (tStart <= :zstart AND tEnd >= :zend))
-                  SQL
-                else
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
-AND  (tEnd BETWEEN :zstart AND :zend))
-                  SQL
-                end
-                cond = {
-                  :chrom  => interval.chrom,
-                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
-                  :zstart => zstart,
-                  :zend   => zend,
-                }
-                self.find(first_all,
-                          { :select => "*",
-                            :conditions => [where, cond], })
-              end
-            end
-          !
-        end # each chromosome
-
-        def self.find_by_interval(interval, opt = {:partial => true})
-          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
-          chr_klass = self.const_get("#{chrom}_#{KLASS}")
-          chr_klass.__send__(:find_by_interval, interval, opt)
-        end
-
-        def self.find_all_by_interval(interval, opt = {:partial => true})
-          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
-          chr_klass = self.const_get("#{chrom}_#{KLASS}")
-          chr_klass.__send__(:find_all_by_interval, interval, opt)
-        end
-      end # class
-
-    end # module Hg18 
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/xentro2/chaingalgal3link.rb

@@ -1,81 +0,0 @@
-# Copyright::
-#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
-#
-# In the hg18 database, this table is actually separated
-# into "chr1_*", "chr2_*", etc. This class dynamically
-# define *::Chr1_*, *::Chr2_*, etc. The
-# Rmsk.find_by_interval calls an appropreate class automatically.
-
-module Bio
-  module Ucsc
-    module TaeGut1
-
-      class ChainGalGal3Link
-        KLASS = "ChainGalGal3Link"
-        KLASS_S = KLASS[0..0].downcase + KLASS[1..-1]
-
-        Bio::Ucsc::GalGal3::CHROMS.each do |chr|
-          class_eval %!
-            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
-
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-        
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
-
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
-                zstart = interval.zero_start
-                zend   = interval.zero_end
-                if opt[:partial] == true
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
- OR  (tEnd BETWEEN :zstart AND :zend)
- OR  (tStart <= :zstart AND tEnd >= :zend))
-                  SQL
-                else
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
-AND  (tEnd BETWEEN :zstart AND :zend))
-                  SQL
-                end
-                cond = {
-                  :chrom  => interval.chrom,
-                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
-                  :zstart => zstart,
-                  :zend   => zend,
-                }
-                self.find(first_all,
-                          { :select => "*",
-                            :conditions => [where, cond], })
-              end
-            end
-          !
-        end # each chromosome
-
-        def self.find_by_interval(interval, opt = {:partial => true})
-          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
-          chr_klass = self.const_get("#{chrom}_#{KLASS}")
-          chr_klass.__send__(:find_by_interval, interval, opt)
-        end
-
-        def self.find_all_by_interval(interval, opt = {:partial => true})
-chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
-          chr_klass = self.const_get("#{chrom}_#{KLASS}")
-          chr_klass.__send__(:find_all_by_interval, interval, opt)
-        end
-      end # class
-
-    end # module Hg18 
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/xentro2/db_connection.rb

@@ -1,57 +0,0 @@
-#
-# = db_connection.rb - UCSC DB connection
-#
-# Copyright::   Cioyrught (C) 2011
-#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# Copyright::   Copyright (C) 2010
-#               Jan Aerts <jan.aerts@gmail.com>
-# License::     Ruby licence (Ryby's / GPLv2 dual)
-
-require 'rubygems'
-require 'active_record'
-
-module Bio
-  module Ucsc
-
-    module XenTro2
-      DATABASE_NAME = "xenTro2"
-
-      # = DESCRIPTION
-      # Actual connection established to the UCSC mysql server.
-      class DBConnection < ActiveRecord::Base
-        # = DESCRIPTION
-        # The #connect method make the connection
-        #
-        # = USAGE
-        #  Bin::Ucsc::DB_NAME::DBConnection.connect
-        #
-        # ---
-        # *Arguments*: none
-        @@db_adapter  ||= 'mysql'
-        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
-        @@db_username ||= 'genome'
-        @@db_password ||= ''
-
-        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
-
-        self.abstract_class = true
-
-        def self.default
-          @@db_adapter  = 'mysql'
-          @@db_host     = 'genome-mysql.cse.ucsc.edu'
-          @@db_username = 'genome'
-          @@db_password = ''
-        end
-
-        def self.connect
-          establish_connection({ :adapter =>  @@db_adapter,
-                                 :host =>     @@db_host,
-                                 :database => DATABASE_NAME,
-                                 :username => @@db_username,
-                                 :password => @@db_password, })
-        end
-      end
-    end # module
-    
-  end # module Ucsc
-end # module Bio

data/lib/bio-ucsc/xentro2/est.rb

@@ -1,81 +0,0 @@
-# Copyright::
-#  Copyright (C) 2011 MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     The Ruby licence (Ryby's / GPLv2 dual)
-#
-# In the hg18 database, this table is actually separated
-# into "chr1_*", "chr2_*", etc. This class dynamically
-# define *::Chr1_*, *::Chr2_*, etc. The
-# Rmsk.find_by_interval calls an appropreate class automatically.
-
-module Bio
-  module Ucsc
-    module TaeGut1
-
-      class Est
-        KLASS = "Est"
-        KLASS_S = "est"
-
-        Bio::Ucsc::TaeGut1::CHROMS.each do |chr|
-          class_eval %!
-            class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
-
-              def self.find_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :first, opt)
-              end
-        
-              def self.find_all_by_interval(interval, opt = {:partial => true})
-                find_first_or_all_by_interval(interval, :all, opt)
-              end
-
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
-                zstart = interval.zero_start
-                zend   = interval.zero_end
-                if opt[:partial] == true
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
- OR  (tEnd BETWEEN :zstart AND :zend)
- OR  (tStart <= :zstart AND tEnd >= :zend))
-                  SQL
-                else
-                  where = <<-SQL
-      tName = :chrom
-AND   bin in (:bins)
-AND ((tStart BETWEEN :zstart AND :zend)
-AND  (tEnd BETWEEN :zstart AND :zend))
-                  SQL
-                end
-                cond = {
-                  :chrom  => interval.chrom,
-                  :bins   => Bio::Ucsc::UcscBin.bin_all(zstart, zend),
-                  :zstart => zstart,
-                  :zend   => zend,
-                }
-                self.find(first_all,
-                          { :select => "*",
-                            :conditions => [where, cond], })
-              end
-            end
-          !
-        end # each chromosome
-
-        def self.find_by_interval(interval, opt = {:partial => true})
-          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
-          chr_klass = self.const_get("#{chrom}_#{KLASS}")
-          chr_klass.__send__(:find_by_interval, interval, opt)
-        end
-
-        def self.find_all_by_interval(interval, opt = {:partial => true})
-          chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
-          chr_klass = self.const_get("#{chrom}_#{KLASS}")
-          chr_klass.__send__(:find_all_by_interval, interval, opt)
-        end
-      end # class
-
-    end # module Hg18 
-  end # module Ucsc
-end # module Bio